Tips and Tricks for Forge

forgeV10.1 was released in March 2013 with a number of new features. We also made a number of improvements to usability and workflow in response to user feedback and our own internal project work. We use our software on an everyday basis for our consulting projects, so we know the difference that these improvements make to everyday tasks.

In this article I’ve highlighted how some of these new features can be put to work in projects. I’ll also go through a couple of tips and tricks that I’ve found useful when working with Forge myself.

One of the key tasks in Forge is to design new molecules and to edit the alignments of existing molecules. Since the molecular editor is used for both these tasks we have simplified how you tell Forge which task you are performing. This is done when you exit the editor – you choose either to save the alignment that you have just created by clicking the “OK” button or you choose to “Process” the molecule and have it aligned to the reference.

If the molecule is saved into the project as an alignment, (you’ve pressed “OK”), you may wish to align the molecule at a later date. This is now easy to do, just select the molecule in the results table, right click and select “Process (Align this molecule)”. The “Processing window” is displayed for you to select how ou want to run the experiment, any existing conformations and alignments are deleted once the new calculation starts.

The functions of the molecule table have been steadily improved over the last few releases. You can now add columns and edit cells as well as sort or filter the table. We plan to continue to enhance the table with features such as pasting data in from other applications such as Excel but would welcome feedback on other features that you would like.

Right clicking on a molecule in the results table gives access to many commands in addition to those described above. For example if you have loaded a molecule file straight into Forge then it will not have been aligned. Using the right click menu you can now choose to promote any alignment of any molecule up to a reference molecule. Alternatively you can copy the alignment to the clipboard or delete it entirely.

The “Mark as aligned” entry can be used to convert the current coordinates of a molecule into an alignment, which is useful when you’ve read in structures that were aligned elsewhere, e.g., by protein sequence alignment. If you have a structure with conformations but no alignments (either from a file or by deleting alignments for a molecule) then the “Mark as aligned” right click menu entry will convert the conformations into alignments enabling a visual inspection of the population.

In Forge, molecules belong to “sets” that are named for QSAR. However, you can use these sets to separate out your dataset in whichever way works for you. For instance, you could load different chemical series into each of the sets or split molecules by activity into different sets. You can put molecules into a set at any time, for example when you find an interesting result you can simply drag and drop it into one of the other molecule sets (or use the right click menu to change its “role”) to have it saved separately. We are planning to enhance this feature in future versions to provide a customizable list of sets that you can rename, but we are keen to hear of other ways we can improve this feature.

The last feature of Forge that I want to highlight here is the capability to manage which columns are displayed in the results table. If you load datasets with a large number of data fields then the “manage columns” feature, accessible by right clicking on any column title, is critical to getting the view of your compounds that you want. Using this feature, you can reorder columns and select which to show and which to hide in the main results table.

We hope that you will find these improvements and tips as useful as we do. Contact us with more suggestions about new features, or workflow and usability improvements that you would like to see in future versions of Forge.

Dr Tim Cheeseright,
Director of Products